Re: [gmx-users] How to obtain a approperiate PDB file of DNA?

is a city to the building of which every human being brought a stone. -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090410/937f6a4a/attachment.html

Re: [gmx-users] LINCS warnings generated in NPT ensemble and not in NVT

Lee Soin wrote: Hello! I'm using COM pulling with distance constraint between two domains of a protein. The energy minimization and a 100-ps equilibrating process in the NPT ensemble with position restraints on protein atoms all passed OK. Then I applied a distance constraint between COM of

[gmx-users] questions regarding Replica Exchange

 Hi, I have few queries regarding Replica Exchange MD. 1) I have 17 replicas , and the files are named as md_0.trr,..,.md_16.trr.Replica exchange is attempted every 100ps. Thus starting from 0, upto 100ps, the coordinates, velocities etc. that are written in md_0.trr files

Re: [gmx-users] questions regarding Replica Exchange

sarbani chattopadhyay wrote: Hi, I have few queries regarding Replica Exchange MD. 1) I have 17 replicas , and the files are named as md_0.trr,..,.md_16.trr.Replica exchange is attempted every 100ps. Thus starting from 0, upto 100ps, the coordinates, velocities etc. that are

Re: [gmx-users] LINCS warnings generated in NPT ensemble and not in NVT

The difference between restraints and constraints is indeed something I'm aware of :-) Even though distance restraint between COM of two domains worked just OK for me, I would prefer to use distance constraint since that will introduce fewer artifacts and can fix the distance between two domains

[gmx-users] define atoms

Dear mark excuse me. I attempt it again.in analysis result of md peptide I have the table t consist of atoms number column and the other column rmsd(nm).I want to know what is thename of atom which define number 12 in backbone group ?Is it NCC for example related to ser or another

Re: [gmx-users] Release of R.E.D. Server

Quoting Joe Joe ilcho...@gmail.com: What about use for commercial purposes? So far, commercial users can use the R.E.D.-III.2 tools which are distributed in the standalone version. A specific license agreement has to be signed in this case. regards, Francois On Thu, Apr 9, 2009 at

Re: [gmx-users] define atoms

shahrbanoo karbalaee wrote: Dear mark excuse me. I attempt it again.in analysis result of md peptide I have the table t consist of atoms number column and the other column rmsd(nm).I want to know what is thename of atom which define number 12 in backbone group ?Is it NCC for example

Re: [gmx-users] Re: Free energy with Gromacs.

You may also want to look at www.alchemistry.org, as it has some general information about how these should be set up. On Wed, Mar 18, 2009 at 8:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: Again, *please keep all Gromacs-related correspondence on the mailing list*  The type of information

[gmx-users] Pressure Coupling Problem

Alright, sorry that I wasn't able to help. I'm confused by some apparent contradictions in your posts and I'm not sure that I'm going to be useful to you here. Quoting http://www.gromacs.org/pipermail/gmx-users/2009-April/041173.html: No matter how much minimization I do the volume of

[gmx-users] Query

Hi, i am running MD on a system where a protien and a small peptide chain are placed closely. After running the simulation when i was analyzing the system, i got a rmsd plot with numerous bumps. For creating the xtc file i tried different options like -pbc nojump/whole etc and also -center

RE: [gmx-users] What's the max number of pull groups?

Thanks so much, Berk. I have another question regarding the pull code. Can I define a pull group that contains more than one molecules? I tried to define some lipid molecules as a single pull group and pull them out of a bilayer. But I couldn't see the lipids out. If I try one lipid as a pull

[gmx-users] mdrun_mpi error Signal: Segmentation fault

I have segmentation fault error while running mdrun_mpi( gromacs 4.0.4). I have installed gromacs 4.0.4 two month ago and been working fine. Today, I just got Segment errors. Rebooting does not much help. Here is log: [rd:06790] *** Process received signal *** [d:06790] Signal: Segmentation

Re: [gmx-users] mdrun_mpi error Signal: Segmentation fault

nam kim wrote: I have segmentation fault error while running mdrun_mpi( gromacs 4.0.4). I have installed gromacs 4.0.4 two month ago and been working fine. Today, I just got Segment errors. Rebooting does not much help. Here is log: [rd:06790] *** Process received signal *** [d:06790]

[gmx-users] x2top: duplicate bond, angle, dihedral parameters; missing VdW parameters

Dear All, I ran the x2top command and successfully generated a topology. However, the topology file has duplicate bond, angle, and dihedral parameters and missing Van der Waals parameters. I am including sections of my topology file for your perusal. Please let me know why this is occurring and

[gmx-users] Replica Exchange Error

Hi All, I get the following error when running replica exchange. I have 32 replica's with each replica running on 4 processors (128 total). How do I decrease the domain decomposition cell size, -dss? What should I set it to? Thanks, Ilya DD cell 2 0 0: Neighboring cells do not have atoms: 22217

Re: [gmx-users] Replica Exchange Error

Joe Joe wrote: Hi All, I get the following error when running replica exchange. I have 32 replica's with each replica running on 4 processors (128 total). How do I decrease the domain decomposition cell size, -dss? What should I set it to? snip You're getting some hints from mdrun, I'd

Re: [gmx-users] Replica Exchange Error

How do I determine what those values should be? How does it affect the simulation? thanks, Ilya On Fri, Apr 10, 2009 at 8:00 PM, Justin A. Lemkul jalem...@vt.edu wrote: Joe Joe wrote: Hi All, I get the following error when running replica exchange. I have 32 replica's with each replica